Covid-19

library(tidyverse)

Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      
── Attaching packages ──────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──
✓ ggplot2 3.3.2     ✓ purrr   0.3.4
✓ tibble  3.0.3     ✓ dplyr   1.0.2
✓ tidyr   1.1.2     ✓ stringr 1.4.0
✓ readr   1.3.1     ✓ forcats 0.5.0
── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()

library(streamgraph)
library(plotly)

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

data <- read.csv('https://covid.ourworldindata.org/data/owid-covid-data.csv')
yesterday <- Sys.Date() - 1
today <- Sys.Date()
data_cleaned <- data %>%
  select(iso_code, continent, location, total_cases, total_deaths, new_deaths, date) %>%
  filter(date== yesterday & location != "World")
#data_cleaned$date <- as.Date(data_cleaned$date)

data_cleaned$hover <- with(data_cleaned, paste(location, '<br>', 
                                               "Total Cases: ", total_cases, '<br>', 
                                               "Total Deaths: ", total_deaths, '<br>', 
                                               "Date: ", date))
# light grey boundaries
l <- list(color = toRGB("grey"), width = 0.5)
# specify map projection/options
g <- list(
  showframe = FALSE,
  showcoastlines = FALSE,
  projection = list(type = 'Mercator'))

fig <- plot_geo(data_cleaned) %>% 
  add_trace(
    z = ~total_deaths, color = ~total_deaths, text = ~hover, colors = 'Reds',
    text = ~location, locations = ~iso_code, marker = list(line = l)) %>% 
  colorbar(title = 'Total Deaths') %>% 
  layout(
    title = 'Covid Data by Country<br>(Hover for breakdown)<br>
            Source:<a href="https://covid.ourworldindata.org/data/owid-covid-data.csv">Our World in Data</a>',
    dragmode= FALSE,
    geo = g
  )

Ignoring 15 observations

fig

#htmlwidgets::saveWidget(fig, "fig_plot_geo.html")

sg_data <- data %>%
  filter(grepl("^(Asia|Africa|Oceania|North America|South America|Europe)$", continent)) %>%
  group_by(date, continent) 

total_deaths_by_continent <- sg_data %>%
  tally(wt= total_deaths) %>%
  streamgraph("continent", "n", "date", offset= "zero", height= 400, width= "100%") %>%
  sg_fill_brewer(palette = "RdBu") %>%
  sg_legend(show = TRUE, label = "Continent:")
total_deaths_by_continent

#htmlwidgets::saveWidget(total_deaths_by_continent, "total_deaths_by_continent.html")

daily_cases_smoothed_by_continent <- sg_data %>%
  tally(wt= new_cases_smoothed) %>%
  streamgraph("continent", "n", "date", offset= "zero", height= 400, width= "100%") %>%
  sg_fill_brewer(palette = "Greens") %>%
  sg_legend(show = TRUE, label = "Continent:")
daily_cases_smoothed_by_continent

#htmlwidgets::saveWidget(daily_cases_smoothed_by_continent, "daily_cases_smoothed_by_continent.html")

daily_deaths_smoothed_by_continent <- sg_data %>%
  tally(wt= new_deaths_smoothed) %>%
  streamgraph("continent", "n", "date", height= 400, width= "100%") %>%
  sg_fill_brewer(palette = "Greens") %>%
  sg_legend(show = TRUE, label = "Continent:")
daily_deaths_smoothed_by_continent

#htmlwidgets::saveWidget(daily_deaths_smoothed_by_continent, "daily_deaths_smoothed_by_continent.html")

state_covid_data <- read.csv('https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv') %>% 
  filter(date== yesterday)

state_codes <- read.csv("https://raw.githubusercontent.com/plotly/datasets/master/2011_us_ag_exports.csv") %>%
  select(state, code)

state_covid_data <- merge(state_codes, state_covid_data)

state_covid_data$hover <- with(state_covid_data, paste(state, '<br>',
                           'Total Cases: ', cases, '<br>',
                           'Total Deaths: ', deaths, '<br>',
                           'Date: ', date))
# give state boundaries a white border
l <- list(color = toRGB('grey'), width = 0.5)
# specify some map projection/options
g <- list(
  scope = 'usa',
  projection = list(type = 'albers usa')
)

fig1 <- plot_geo(state_covid_data, locationmode = 'USA-states') %>% 
  add_trace(
    z = ~deaths, text = ~hover, locations = ~code,
    color = ~deaths, colors = 'Reds', marker = list(line = l)
  ) %>%
colorbar(title = 'Total Deaths') %>% 
  layout(
    title = "Covid Data by State<br>(Hover for breakdown)<br>
            Source:<a href='https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv'>New York Times</a>",
    dragmode= FALSE,
    geo = g
  )
fig1

#htmlwidgets::saveWidget(fig1, "fig_plot_geo1.html")

data <- data %>%
  filter(location != "World")
x <- list(title = "Date")

y <- list(title= "Total Deaths")

tx <- highlight_key(data, ~location)

fig2 <- plot_ly(tx, color = I("Black"), height = 500) %>% 
  group_by(location) %>%
  add_lines(x = ~date, y = ~total_deaths) %>%
  layout(
    xaxis= x, 
    yaxis= y,
    title = 'Covid Data by Country<br>(Hover for breakdown)<br>
            Source:<a href="https://covid.ourworldindata.org/data/owid-covid-data.csv">Our World in Data</a>'
    )

`group_by_()` is deprecated as of dplyr 0.7.0.
Please use `group_by()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.

fig2 <- plotly::highlight(
  fig2, 
  on = "plotly_click", 
  selectize = TRUE, 
  dynamic = TRUE, 
  persistent = TRUE,
  color = NULL
)

Adding more colors to the selection color palette.
We recommend setting `persistent` to `FALSE` (the default) because persistent selection mode can now be used by holding the shift key (while triggering the `on` event).

fig2

Setting the `off` event (i.e., 'plotly_doubleclick') to match the `on` event (i.e., 'plotly_click'). You can change this default via the `highlight()` function.
Setting the `off` event (i.e., 'plotly_doubleclick') to match the `on` event (i.e., 'plotly_click'). You can change this default via the `highlight()` function.

htmlwidgets::saveWidget(fig, "fig_plot_geo.html")
htmlwidgets::saveWidget(fig1, "fig_plot_geo1.html")
#htmlwidgets::saveWidget(fig2, "fig_plot_geo2.html")
htmlwidgets::saveWidget(total_deaths_by_continent, "total_deaths_by_continent.html")

?color